Code for Lecture 8 - occupancy analysis in R library(unmarked) #occupancy analysis in R requires the unmarked library ###Import the Data from the web site datumOcc=read.csv(file.choose()) ###This is your occupancy data datumSite=read.csv(file.choose()) ###This is your site covariates (1 column per variable) datumObs=read.csv(file.choose()) ###This is your observation covariates (1 column per variable per observation) ###create unmarkedFrame - needs matrix of detection histories, matrix of site covariates, and matrix of observation #covariates in long format datum=unmarkedFrameOccu(y=datumOcc,siteCovs=datumSite,obsCovs=datumObs) summary(datum) #spits out some basic summary stats of unmarkedframe ###First run a naive model with no variables results=occu(~1 ~1,datum) summary(results) ###A model with unconstrained detection probabilities, and no site covariate results=occu(~Day2+Day3 ~1, datum) summary(results) ###A model with no observation covariate, and site covariate "distance" results=occu(~1 ~Distance, datum) summary(results) ###A model with unconstrained detection probabilities and site covariate "distance" results=occu(~Day2+Day3 ~Distance, datum) summary(results) ###A model with observation covariate "Temp" and no site covariate results=occu(~Temp ~1, data=datum) summary(results)